Comments (5)
I need a bit more information to figure out where the problem could be.
- Are you using the same standalone version as what is run on the webserver?
- In which way are the results different?
- Do you have a reproducible example I can use for testing?
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Hi
I will answer point by point. As for the difference between web server and standalone, how specifically are the outputs different? Do you use some non-default parameters on either the standalone or webserver?
- You could put them all in one fasta and run cctyper with
--prodigal meta
, but it's faster to parallelize across MAGs with for example GNU parallel - There is a Cas9 HMM that matches both II-A and II-C, hence it's ambiguous
- Not sure what you mean by a false positive column?
- Unknown gene means that it is not CRISPR-Cas related
- It's an operon with two cas9, or maybe it should have been one gene but the ORF was called wrongly
- That sounds like a mistake, could you send one of the figures? Also, is it only for specific subtypes or for different subtypes?
Cheers,
Jakob
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Please find the image showing Cas1 in purple. It is for all subtypes
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The Cas1 gene has the expected color. All adaptation related genes will have this color (blur, purple, or what you want to call it).
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Related Issues (20)
- Complete genome and draft genome HOT 2
- A complement to CRISRPRCasFinder or its own thing? HOT 1
- Execution against protein fasta and gff HOT 2
- Error when running cctyper: sed: cannot rename <output filename>/sed78a7GM: Permission denied HOT 2
- ![image](https://user-images.githubusercontent.com/121949837/212599561-d771b233-4bde-4850-8e5f-98a4164f78cb.png)
- Option to use Prodigal-gv
- Meaning of asterisk at the end of protein sequence HOT 1
- Creating empty files when there's no data HOT 1
- castyping.py having an issue with positional arguments. HOT 2
- CCTyper results HOT 4
- Orphan CRISPR definition HOT 2
- (Question) provide GFF file for pre computed gene calls? HOT 5
- XGBoost model incompatible HOT 8
- If minced detects a CRISPR with N's in the repeat sequence
- (Question) How can I plot svg post-hoc after a run? HOT 1
- ValueError: invalid literal for int() with base 10: 'lengt' HOT 2
- access to sequences that used to geenrate Cas profiles
- access to sequences that used to geenrate Cas profiles HOT 1
- error while loading shared libraries: libnsl.so.1
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